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- PDB-3lx7: Crystal structure of a Novel Tudor domain-containing protein SGF29 -

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Basic information

Entry
Database: PDB / ID: 3lx7
TitleCrystal structure of a Novel Tudor domain-containing protein SGF29
ComponentsSAGA-associated factor 29 homolog
KeywordsTRANSCRIPTION REGULATOR / SAGA / Tudor / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair ...SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / transcription initiation-coupled chromatin remodeling / methylated histone binding / response to endoplasmic reticulum stress / mitotic spindle / HATs acetylate histones / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
SAGA-associated factor 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBian, C.B. / Xu, C. / Tempel, W. / Lam, R. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Min, J.
CitationJournal: Embo J. / Year: 2011
Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation.
Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAGA-associated factor 29 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8466
Polymers19,7501
Non-polymers965
Water81145
1
A: SAGA-associated factor 29 homolog
hetero molecules

A: SAGA-associated factor 29 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,69212
Polymers39,5002
Non-polymers19210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1930 Å2
ΔGint-39 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.802, 51.290, 44.842
Angle α, β, γ (deg.)90.00, 117.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SAGA-associated factor 29 homolog / Coiled-coil domain-containing protein 101


Mass: 19750.080 Da / Num. of mol.: 1 / Fragment: Residues 138-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC101, SGF29 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96ES7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.34 % / Mosaicity: 0.432 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 0.2M potassium sodium tartrate, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 13275 / % possible obs: 91.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.071 / Χ2: 2.367 / Net I/av σ(I): 26.236 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.820.3014271.337159.5
1.8-1.832.20.2344651.106165.6
1.83-1.872.40.2255651.294176.5
1.87-1.912.70.2125841.427180.7
1.91-1.9530.2026251.304187.2
1.95-1.993.10.1856511.373190.7
1.99-2.043.20.1616891.556193.6
2.04-2.13.30.1426911.848196.9
2.1-2.163.40.1327111.85198.2
2.16-2.233.40.1237221.861199
2.23-2.313.60.1247232.012199.7
2.31-2.43.70.1137232.09199.9
2.4-2.513.70.0987482.1041100
2.51-2.643.70.0897292.3441100
2.64-2.813.80.0787202.5111100
2.81-3.033.70.0697323.054199.6
3.03-3.333.70.0617223.412199.3
3.33-3.813.60.0517143.326196.4
3.81-4.83.40.0436293.241185.9
4.8-503.40.0497054.944191.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ME9

3me9


Resolution: 1.78→25.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.169 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 667 5 %RANDOM
Rwork0.20647 ---
obs0.20848 12587 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.679 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.04 Å2
2--0.22 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.78→25.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 9 45 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221160
X-RAY DIFFRACTIONr_bond_other_d0.0020.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9711593
X-RAY DIFFRACTIONr_angle_other_deg0.88131875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8223.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64715162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.132157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8971.5727
X-RAY DIFFRACTIONr_mcbond_other0.2371.5277
X-RAY DIFFRACTIONr_mcangle_it1.64921176
X-RAY DIFFRACTIONr_scbond_it2.5583433
X-RAY DIFFRACTIONr_scangle_it4.2534.5415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.78-1.8260.436330.2566160.264106560.9390.213
1.826-1.8760.303370.2437320.246104773.4480.206
1.876-1.930.289430.2347680.23799481.590.193
1.93-1.9890.184400.2198450.21797990.3980.171
1.989-2.0540.264450.2018530.20496892.7690.17
2.054-2.1260.195370.1798440.1890697.2410.155
2.126-2.2060.184480.198310.18989298.5430.17
2.206-2.2950.227410.1798030.18184599.8820.158
2.295-2.3970.185420.2018100.285499.7660.182
2.397-2.5130.303360.2227490.2267851000.204
2.513-2.6480.283370.2036960.20773499.8640.192
2.648-2.8070.17380.2136750.2117131000.207
2.807-2.9990.234440.2126280.21367499.7030.21
2.999-3.2370.26400.2115790.21462299.5180.219
3.237-3.5410.259230.2065350.20856698.5870.216
3.541-3.9530.28250.1914750.19653094.340.209
3.953-4.5510.198170.1693790.1747084.2550.184
4.551-5.5420.262170.1843290.18839088.7180.206
5.542-7.7070.31170.2422900.24631497.7710.282
7.707-300.27270.3361500.33319082.6320.412
Refinement TLS params.Method: refined / Origin x: 12.1841 Å / Origin y: 0.794 Å / Origin z: 18.4979 Å
111213212223313233
T0.078 Å2-0.0007 Å2-0.0143 Å2-0.019 Å2-0.0042 Å2--0.0639 Å2
L4.3582 °21.0746 °2-0.8022 °2-1.4668 °2-0.2196 °2--1.2382 °2
S-0.0438 Å °0.2065 Å °-0.0701 Å °-0.0415 Å °0.0773 Å °0.0681 Å °-0.0087 Å °-0.1309 Å °-0.0334 Å °

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